scPDB - 3zhv entry

Protein Data Bank Entry:

PDB ID : 3zhv

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2012-12-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Multifunctional 2-oxoglutarate metabolism enzyme
ID:	KGD_MYCS2
AC:	A0R2B1
Organism:	Mycobacterium smegmatis 155)
Reign:	Bacteria
TaxID:	246196
EC Number:	1.2.4.2

Chains:

Chain Name:	Percentage of Residues within binding site
A	31 %
B	69 %

Ligand binding site composition:

B-Factor:	39.965
Number of residues:	38
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.063	1437.750

% Hydrophobic	% Polar
41.55	58.45
According to VolSite

Ligand :

HET Code:	TDW
Formula:	C14H20N4O8P2S
Molecular weight:	466.343 g/mol
DrugBank ID:	-
Buried Surface Area:	68.21 %
Polar Surface area:	245.55 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
5.73162	-14.7127	-43.1413

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O1B	NE	ARG- 540	3.09	174.87	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 540	3.08	163.26	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 540	3.93	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 540	3.94	0	Ionic (Protein Cationic)	false
N4'	O	SER- 604	2.64	172.72	H-Bond (Ligand Donor)	false
CM2	CB	HIS- 605	4.26	0	Hydrophobic	false
S1	CD1	LEU- 606	4.17	0	Hydrophobic	false
C5'	CD1	LEU- 606	4.25	0	Hydrophobic	false
CM4	CD1	LEU- 606	4.48	0	Hydrophobic	false
C7	CD1	LEU- 606	3.53	0	Hydrophobic	false
N3'	N	LEU- 606	3.05	166.1	H-Bond (Protein Donor)	false
O2A	N	ALA- 646	3	161.9	H-Bond (Protein Donor)	false
O1A	N	ALA- 647	3.01	149.26	H-Bond (Protein Donor)	false
O3B	ND2	ASN- 678	3.03	149.28	H-Bond (Protein Donor)	false
C6	CB	PHE- 682	4.22	0	Hydrophobic	false
CM4	CG	GLN- 901	4.39	0	Hydrophobic	false
CM2	CD2	LEU- 950	4.47	0	Hydrophobic	false
CM4	CD1	LEU- 950	3.56	0	Hydrophobic	false
C7	CD1	LEU- 950	3.62	0	Hydrophobic	false
N1'	OE2	GLU- 952	2.82	153.16	H-Bond (Ligand Donor)	false
C29	CE1	PHE- 977	4.14	0	Hydrophobic	false
CM2	CD1	PHE- 980	4.26	0	Hydrophobic	false
DuAr	DuAr	PHE- 980	3.78	0	Aromatic Face/Face	false
O28	NE2	HIS- 1020	3	157.82	H-Bond (Protein Donor)	false
O2A	MG	MG- 2002	2.07	0	Metal Acceptor	false
O3B	MG	MG- 2002	2.21	0	Metal Acceptor	false
O1B	O	HOH- 3062	2.79	140.91	H-Bond (Protein Donor)	false